TB-Profiler result

Run: ERR4814700
Summary

Run ID: ERR4814700

Sample name:

Date: 01-04-2023 13:26:34

Number of reads: 446013

Percentage reads mapped: 58.88

Strain: lineage4.3.3

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.99
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.4 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.58 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.55 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.5 kanamycin, capreomycin, aminoglycosides, amikacin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 6994 c.-308C>T upstream_gene_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7850 c.549C>G synonymous_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490928 p.Gly49Val missense_variant 0.29
ccsA 619734 c.-157C>A upstream_gene_variant 1.0
rpoB 762879 p.Met1025Leu missense_variant 0.33
rpoC 762902 c.-468C>T upstream_gene_variant 0.5
rpoC 762911 c.-459C>T upstream_gene_variant 0.62
rpoC 762917 c.-453C>T upstream_gene_variant 0.62
rpoC 762920 c.-450C>T upstream_gene_variant 0.62
rpoC 762929 c.-441G>T upstream_gene_variant 0.62
rpoC 762944 c.-426C>T upstream_gene_variant 0.56
rpoC 762956 c.-414G>T upstream_gene_variant 0.5
rpoC 762962 c.-408C>T upstream_gene_variant 0.44
rpoC 762983 c.-387C>T upstream_gene_variant 0.3
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779379 c.-899C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781760 c.201T>C synonymous_variant 0.17
rpsL 781766 c.207C>T synonymous_variant 0.15
rpsL 781772 c.213C>T synonymous_variant 0.17
rpsL 781796 p.Met79Ile missense_variant 0.14
rpsL 781802 c.243G>C synonymous_variant 0.14
rpsL 781805 c.246G>T synonymous_variant 0.14
rpsL 781811 c.252C>T synonymous_variant 0.14
rpsL 781814 c.255C>T synonymous_variant 0.14
rpsL 781817 c.258G>T synonymous_variant 0.14
rpsL 781829 c.270G>C synonymous_variant 0.15
rpsL 781832 c.273T>C synonymous_variant 0.15
rpsL 781838 c.279G>T synonymous_variant 0.17
rplC 800908 p.Asn34Asp missense_variant 0.22
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.25
Rv1258c 1406946 p.Ala132Gly missense_variant 0.25
Rv1258c 1406948 c.391_392delGC frameshift_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.36
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.47
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.31
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.53
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.53
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.15
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.16
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.19
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.94
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.14
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.81
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.19
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.96
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 1.0
rrs 1472379 n.534T>C non_coding_transcript_exon_variant 1.0
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 1.0
rrs 1472416 n.571C>T non_coding_transcript_exon_variant 1.0
rrs 1472422 n.577T>C non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.4
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.29
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.29
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.59
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.62
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.63
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.63
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.26
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.62
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.27
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.67
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.62
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.98
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.28
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.62
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.62
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.31
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.67
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.14
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.8
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.83
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.44
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.56
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.5
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.43
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 1.0
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.93
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.61
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.29
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.6
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.59
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.57
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.29
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.62
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.4
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.49
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.48
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.9
rrs 1472825 n.980G>A non_coding_transcript_exon_variant 0.44
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.33
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1472892 n.1047T>C non_coding_transcript_exon_variant 0.2
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 1.0
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.2
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.7
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.2
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.1
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.7
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.8
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 1.0
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.83
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.86
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.76
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.91
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.1
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.97
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 1.0
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.97
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.97
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.12
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.97
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.95
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.94
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.93
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.93
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.93
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.93
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.8
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.94
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.11
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.16
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.97
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.11
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.11
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.93
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.12
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.11
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.11
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.11
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.73
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.67
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.46
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.7
rrs 1473291 n.1446G>A non_coding_transcript_exon_variant 0.22
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.8
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.55
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.86
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 1.0
rrl 1474883 n.1226T>C non_coding_transcript_exon_variant 1.0
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.5
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.5
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 0.5
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.8
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.8
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.8
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 1.0
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.75
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 1.0
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 1.0
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 1.0
rrl 1476253 n.2596A>G non_coding_transcript_exon_variant 1.0
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 1.0
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.92
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.95
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.96
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.94
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.86
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.9
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.86
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.5
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.5
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.5
rrl 1476600 n.2943A>T non_coding_transcript_exon_variant 0.5
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.5
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.5
rrl 1476616 n.2959A>G non_coding_transcript_exon_variant 0.5
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.5
rrl 1476628 n.2971T>G non_coding_transcript_exon_variant 0.5
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.5
rrl 1476633 n.2976A>G non_coding_transcript_exon_variant 0.5
rrl 1476664 n.3007T>A non_coding_transcript_exon_variant 0.67
rpsA 1834195 c.654G>C synonymous_variant 0.18
rpsA 1834210 c.669C>T synonymous_variant 0.14
rpsA 1834213 c.672G>A synonymous_variant 0.14
rpsA 1834219 c.678C>G synonymous_variant 0.14
rpsA 1834222 c.681T>C synonymous_variant 0.14
rpsA 1834225 c.684C>G synonymous_variant 0.15
rpsA 1834228 c.687C>T synonymous_variant 0.23
rpsA 1834231 c.690T>C synonymous_variant 0.15
rpsA 1834246 c.705G>T synonymous_variant 0.21
rpsA 1834249 c.708T>C synonymous_variant 0.21
rpsA 1834252 c.711C>T synonymous_variant 0.15
rpsA 1834261 c.720A>G synonymous_variant 0.3
rpsA 1834264 c.723G>C synonymous_variant 0.27
rpsA 1834285 c.744G>C synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103090 c.-48G>T upstream_gene_variant 0.14
Rv1979c 2222989 p.Gly59Asp missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518438 c.325delG frameshift_variant 0.29
kasA 2518919 p.Gly269Ser missense_variant 1.0
pepQ 2860240 p.Tyr60Cys missense_variant 0.12
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448854 c.351C>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568773 c.-94G>C upstream_gene_variant 0.33
alr 3840265 p.Ile386Val missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040546 c.159G>A synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249371 p.Leu953Gln missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407865 c.337delG frameshift_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0